EMBOSS: Project Meeting (Mon 15th Aug 11)


EBI: Peter Rice, Mahmut Uludag
Apologies: Alan Bleasby, Jon Ison, Michael Schuster

1. Minutes of the last meeting

Minutes of the meeting of 8th August 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter has added reference sequence and assembly applications, called refseqget and assemblyget, plus an application variationget for variation data.

Peter has installed mira release 3.4rc3 for testing. >b>Mahmut is testing assembly formats in mira 3.2.

2.2 Libraries

Peter has extended the query language syntax to allow more flexible ways to append a sequence range. Both ":start:end" and ":start..end" are allowed each with a ":r" suffix to reverse the range.

2.3 Other

Peter has renamed QA tests to provide a "keep" or "ex" suffix but not both.

3. New developments

3.1 Reference sequences

Peter has written a parser for CON (contig) entries in EMBL which picks up the individual sequence regions and builds a complete sequence. Some CON entries in EMBL were found to refer to renamed entries. The ENA support desk has been notified. The entries are owned by the submitters, so they have been asked to update the CON entries to match the renamed whole genome shotgun (WGS) fragments.

Peter will consider qualifier names to control the resolution of reference sequence and assembly inputs (reading the sequence only if resolution is to the level of individual bases).

The AjPRefseq data object includes a list of sequence fragments with position and length so we can later read a specified region without loading the entire sequence.

3.2 Ensembl

Peter has defined a new database attribute "special:" which can appear multiple times in a database definition. The value is a "name-value" where the name is specific to the assembly method. This can include the species ID currently defined as a comment in 6.4.0 for Ensembl genomes.

4. Administration

Alan has reported releasing the first set of patches to 6.4.0 and a new mEMBOSS build

Peter will ask the SAB for suggestions on a new homepage for the website.

5. Documentation and Training

5.1 Web server

5.2 Books

6. User queries and answers

All done.

7. AOB


8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 22nd August.